Plant defense after flooding

Abstract

Since the first study of hypoxic response in plants with cDNA microarray in 2002, the number of hypoxia-responsive genes has grown to more than 2000. However, to date, only small numbers of hypoxia-responsive genes are known to confer hypoxic resistance. Most investigations in this area have focused on identifying which genes are responsive and then characterized how these genes are induced during hypoxia, but the roles of numerous genes in hypoxic response are still unknown. In our recent study, we demonstrated that a group of genes are induced by submergence to trigger plant immunity, which is a response to protect plants against a higher probability of pathogen infection during or after flooding. This work offered a brand new perspective, i.e., that hypoxia-responsive genes can be induced for reasons other than conferring hypoxic resistance. Possible reasons why these responses were triggered are discussed herein.

In natural environments, plants encounter multiple stresses due to their immobility. However, most studies have focused on elucidating mechanisms against a single stress. To ensure their survival, plants must evolve mechanisms against multiple stresses. Thus, it is of importance to study mechanisms alongside stresses that usually take place simultaneously or sequentially in the natural environment. Flooding is a complex stress that encompasses many changes in environmental factors, including light intensity, pH, and dissolved oxygen concentration. After flooding gives way, plants have to deal with further follow-up environmental changes, including higher oxidative stress when re-oxygenated, a higher probability of pathogen infection, and leaching of nutrients in soils. Despite the fact that plants face so many stresses upon/after flooding, the majority of studies have focused solely on responses to oxygen deprivation and explained mechanisms of flooding resistance based on how plants deal with hypoxic conditions.

Why is the expression of a large number of genes altered upon flooding?

Traditionally, it is believed that the major stress factor upon flooding is oxygen deprivation, which triggers plant induction of the expression of fermentative and glycolytic genes to cope with energy deprivation when cellular respiration is blocked. Accumulating evidence further suggests that multiple signaling pathways are triggered transcriptionally in response to flooding.^1-5 In 2002, the first transcriptomic study used a microarray containing 3500 cDNA clones to identify 210 differentially expressed genes in response to low-oxygen conditions in Arabidopsis root culture.³ Since then the number of low-oxygen responsive genes identified in Arabidopsis has increased to more than 4000, of which around 2000 genes are upregulated.^6,7 Although a large number of genes are induced upon flooding, only a small number of them are known to play roles in flooding resistance. Data from these transcriptomic studies mostly shows that many flood-induced genes are also induced by other stresses, suggesting overlapping functions of these genes between flooding and other stresses.^3,6-9 However, it is still unclear why so many genes are regulated under flooding and how many of them directly contribute to flooding resistance. A possible reason is that these genes could have co-evolved in response to flooding and be induced against the other environmental changes associated with flooding mentioned above. The co-evolution of such responses is discussed below with reference to the findings presented in our recent publication, “Submergence Confers Immunity Mediated by the WRKY22 Transcription Factor in Arabidopsis.”¹⁰

Defense response co-evolved with flooding

Our recent study showed that many WRKY transcription factors and innate immunity marker genes are rapidly induced upon submergence, suggesting that submergence triggers innate immunity.¹⁰ Plant innate immunity is usually triggered by microbe- or pathogen-associated molecular patterns and/or effector-triggered immunity, but in our case we found that innate immunity was triggered by pathogen-free submergence conditions. This new finding begs the question as to why plants need to boost immunity in response to flooding. Since flooding might lead to a higher probability of pathogen infection in the immediate environment of the plant, we suggested that plants may evolve mechanisms against biotic stresses in response to flooding to anticipate a higher risk of pathogen attack.¹⁰ This new concept of “anticipating infection” was recently presented in another study. Temporal control of plant defense was found to allow plants to anticipate infection at the time of day when a pathogen normally disperses the spores.¹¹ Both this study and our own study support the idea that plants have evolved mechanisms that are sophisticated and intertwined with closely associated environmental conditions.

Transcriptional regulation in common with flooding

When we observe that a gene is individually triggered by 2 environmental conditions, how should we interpret the role of this gene? A classical explanation for the observation is that this gene has an overlapping function under both conditions. If these 2 conditions are intimately related, we could also put forward a theory of co-evolution as hinted at in our recent publication, i.e., the gene could have a function under one condition with its expression being triggered by the other condition to prepare for the follow-up condition. One approach to the investigation of genes that play roles in flooding and/or in other stresses is to identify genes that are co-expressed in flooding and other stresses. Among genes that are co-expressed under flooding and other stresses,^3,6-9 we found that large numbers of genes were co-expressed with biotic stresses, so we further focused on genes encoding WRKY transcription factors and innate immunity markers.¹⁰ Our results not only showed the induction of WRKY genes and innate immunity marker genes in response to flooding, but also showed that pathogen resistance can be triggered by flooding. We further identified a key transcription factor, WRKY22, that mediates this response.¹⁰ From the starting point of identifying genes co-expressed under both biotic stress and flooding, we revealed a mechanism triggered by flooding that allows plants to cope with follow-up pathogen infection. Notably, flooding-triggered gene expression of WRKY transcription factors and innate immunity markers were also induced in drought and salt treatment,¹⁰ suggesting that this transcriptional regulation of immunity may also occur with other stresses in the same way as demonstrated in our study with flooding.

Future challenges

Our study showed that a WRKY-mediated transcriptional regulation triggers plant immunity upon flooding.¹⁰ Although this work provides a new link between flooding and plant defense, the perception and upstream signaling that controls immunity in response to flooding remain unclear. Understanding the upstream signaling pathways may not only resolve how immunity is triggered by flooding, but may also lead to a new model of how plants perceive environmental cues upon flooding. Our work indicated that flooding triggered many genes related to receptor-like kinase (RLK) signaling, including genes encoding molecular patterns, RLKs, and downstream markers of RLKs.¹⁰ Such results are informative hints about new sensing mechanisms for flooding, but how these putative mechanisms work is still unknown. Thus, we are beginning to investigate functions of RLK-related genes with respect to flooding resistance. This may help identify novel sensing mechanisms and signaling pathways in plants upon flooding.

Hsu F-C, Chou M-Y, Chou S-J, Li Y-R, Peng H-P, Shih M-C. Submergence confers immunity mediated by the WRKY22 transcription factor in Arabidopsis. Plant Cell. 2013;25:2699–713. doi: 10.1105/tpc.113.114447.